diagnosis.log

This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013/Debian) (format=pdfetex 2016.2.12)  15 FEB 2016 11:05
entering extended mode
 restricted \write18 enabled.
 %&-line parsing enabled.
**\nonstopmode \catcode126=12 \def\normaltilde{~}\catcode126=13 \let~\normaltil
de  \input ./diagnosis.txt
(./diagnosis.txt
! Missing $ inserted.
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                $
<to be read again> 
                   _
l.6   pdf_
          document:
I've inserted a begin-math/end-math symbol since I think
you left one out. Proceed, with fingers crossed.

! Missing $ inserted.
<inserted text> 
                $
<to be read again> 
                   \par 
l.7 
    
I've inserted a begin-math/end-math symbol since I think
you left one out. Proceed, with fingers crossed.

Missing character: There is no à in font cmr10!
Missing character: There is no ­ in font cmr10!

Overfull \hbox (33.95674pt too wide) in paragraph at lines 10--11
\tenrm HTML, PDF, and MS Word doc-u-ments. For more de-tails on us-ing R Mark-d
own see <http://rmarkdown.rstudio.com>. |

\hbox(7.5+2.5)x469.75499, glue set - 1.0
.\tenrm H
.\tenrm T
.\tenrm M
.\tenrm L
.\tenrm ,
.etc.

! Missing $ inserted.
<inserted text> 
                $
<to be read again> 
                   _
l.16     keep_
              tex: true
I've inserted a begin-math/end-math symbol since I think
you left one out. Proceed, with fingers crossed.

)
! Emergency stop.
<*> ...3 \let~\normaltilde  \input ./diagnosis.txt
                                                  
*** (job aborted, no legal \end found)

!  ==> Fatal error occurred, no output PDF file produced!